The decision puts an end to the European champions’ plans to allow 7,500 fans into the Allianz Arena to watch Friday’s opening game at home to Schalke.
“It would be the wrong signal to let spectators into sports stadiums against the background of the current figures,” said Munich mayor Dieter Reiter.
Germany’s politicians have given Bundesliga clubs the green light to allow the partial return of fans into stadiums, providing the rate of infection in each region remains below 35 per 100,000 inhabitants.
However, the figure for Munich was revised to 47.6 per 100,000 on Thursday.
While the defending champions must kick-off without fans, set numbers of spectators are expected to attend other Bundesliga matches on the opening weekend of the league season.
Reiter said he could understand the frustration of the club and Bayern’s fans, but “for me, this high number means that we at least have to think about much more drastic restrictions in public life.
“I can’t let thousands of fans into the stadiums at the same time.”
Bayern head coach Hansi Flick accepted the news as they start their quest to win their ninth Bundesliga title in a row.
“I’ve always said I’m in favor of keeping an eye on things,” Flick told reporters on Thursday.
“We have to protect ourselves and make the best of the situation.
“You have to take the numbers into account. These are things that I can’t do anything about, we have to be prepared for them.”